B Chromosomes Research Articles

Transcriptome Dynamic Analysis Reveals New Candidate Genes Associated with Resistance to Fusarium Head Blight in Two Chinese Contrasting Wheat Genotypes

In recent years, Fusarium head blight (FHB) has developed into a global disease that seriously affects the yield and quality of wheat. Effective measures to solve this problem include exploring disease-resistant genes and breeding disease-resistant varieties. In this study, we conducted a comparative transcriptome analysis to identify the important genes that are differentially expressed in FHB medium-resistant (Nankang 1) and FHB medium-susceptible (Shannong 102) wheat varieties for various periods after Fusarium graminearum infection using RNA-seq technology. In total, 96,628 differentially expressed genes (DEGs) were identified, 42,767 from Shannong 102 and 53,861 from Nankang 1 (FDR < 0.05 and |log2FC| > 1). Of these, 5754 and 6841 genes were found to be shared among the three time points in Shannong 102 and Nankang 1, respectively. After inoculation for 48 h, the number of upregulated genes in Nankang 1 was significantly lower than that of Shannong 102, but at 96 h, the number of DEGs in Nankang 1 was higher than that in Shannong 102. This indicated that Shannong 102 and Nankang 1 had different defensive responses to F. graminearum in the early stages of infection. By comparing the DEGs, there were 2282 genes shared at the three time points between the two strains. GO and KEGG analyses of these DEGs showed that the following pathways were associated with disease resistance genes: response to stimulus pathway in GO, glutathione metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant-pathogen interaction in KEGG. Among them, 16 upregulated genes were identified in the plant-pathogen interaction pathway. There were five upregulated genes, TraesCS5A02G439700, TraesCS5B02G442900, TraesCS5B02G443300, TraesCS5B02G443400, and TraesCS5D02G446900, with significantly higher expression levels in Nankang 1 than in Shannong 102, and these genes may have an important role in regulating the resistance of Nankang 1 to F. graminearum infection. The PR proteins they encode are PR protein 1-9, PR protein 1-6, PR protein 1-7, PR protein 1-7, and PR protein 1-like. In addition, the number of DEGs in Nankang 1 was higher than that in Shannong 102 on almost all chromosomes, except chromosomes 1A and 3D, but especially on chromosomes 6B, 4B, 3B, and 5A. These results indicate that gene expression and the genetic background must be considered for FHB resistance in wheat breeding.

Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers.

Biofortification is gaining importance globally to improve human nutrition through enhancing the micronutrient content, such as vitamin A, iron, and zinc, in staple food crops. The present study aims to identify the chromosomal regions governing the grain iron concentration (GFeC), grain zinc concentration (GZnC), and thousand kernel weight (TKW) using recombinant inbred lines (RILs) in wheat, developed from a cross between HD3086 and HI1500. The experiment was conducted in four different production conditions at Delhi viz., control, drought, heat, and combined heat and drought stress and at Indore under drought stress. Grain iron and zinc content increased under heat and combined stress conditions, while thousand kernel weight decreased. Medium to high heritability with a moderate correlation between grain iron and zinc was observed. Out of 4,106 polymorphic markers between the parents, 3,407 SNP markers were used for linkage map construction which spanned over a length of 14791.18 cm. QTL analysis identified a total of 32 chromosomal regions governing the traits under study, which includes 9, 11, and 12 QTLs for GFeC, GZnC, and TKW, respectively. A QTL hotspot was identified on chromosome 4B which is associated with grain iron, grain zinc, and thousand kernel weight explaining the phenotypic variance of 29.28, 10.98, and 17.53%, respectively. Similarly, common loci were identified on chromosomes 4B and 4D for grain iron, zinc, and thousand kernel weight. In silico analysis of these chromosomal regions identified putative candidate genes that code for proteins such as Inositol 1,3,4-trisphosphate 5/6-kinase, P-loop containing nucleoside triphosphate hydrolase, Pleckstrin homology (PH) domains, Serine-threonine/tyrosine-protein kinase and F-box-like domain superfamily proteins which play role in many important biochemical or physiological process. The identified markers linked to QTLs can be used in MAS once successfully validated.

QTL Mapping for Wheat Seed Dormancy in a Yangmai16/Zhongmai895 Double Haploid Population.

Pre-harvest sprouting (PHS) of wheat reduces grain yield and quality, and it is strongly affected by seed dormancy. Therefore, identification of quantitative trait loci (QTL) for seed dormancy is essential for PHS resistance breeding. A doubled haploid (DH) population, consisting of 174 lines from the cross between Yangmai16 (YM16) and Zhongmai895 (ZM895) was used to detect QTLs for seed dormancy and grain color. For seed dormancy, a total of seven QTLs were detected on chromosomes 2A, 3A, 3D, 4D, 5B and 5D over four environments, among which Qdor.hzau-3A, Qdor.hzau-3D.1 and Qdor.hzau-3D.2 were stably detected in more than two environments. For grain color, only two QTLs, Qgc.hzau-3A and Qgc.hzau-3D were detected on chromosomes 3A and 3D, which physically overlapped with Qdor.hzau-3A and Qdor.hzau-3D.1, respectively. Qdor.hzau-3D.2 has never been reported elsewhere and is probably a novel locus with allelic effect of seed dormancy contributed by weakly dormant parent ZM895, and a KASP marker was developed and validated in a wheat natural population. This study provides new information on the genetic dissection of seed dormancy, which may aid in further improvement for marker-assisted wheat breeding for PHS resistance.

Centromere repositioning and shifts in wheat evolution

The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms. Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat. Here, we comprehensively analyzed centromeres from the de novo-assembled common wheat cultivar Aikang58 (AK58), Chinese Spring (CS), and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing, whole-genome bisulfite sequencing, RNA sequencing, assay for transposase-accessible chromatin using sequencing, and comparative genomics. We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization. Centromeric repeats of wheat (CRWs) have undergone expansion during wheat evolution, with strong interweaving between the A and B subgenomes post tetraploidization. We found that CENH3 prefers to bind with younger CRWs, as directly supported by immunocolocalization on two chromosomes (1A and 2A) of wild emmer wheat with dicentromeric regions, only one of which bound with CENH3. In a comparison of AK58 with CS, obvious centromere repositioning was detected on chromosomes 1B, 3D, and 4D. The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels. We also found that centromeric chromatin was more open than pericentromeric chromatin, with higher levels of gene expression but lower gene density. Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome. This study also showed that active wheat centromeres were genetically and epigenetically determined.

Identification of the candidate gene controlling tiller angle in common wheat through genome-wide association study and linkage analysis

Wheat tiller angle (TA) is an important agronomic trait that contributes to grain production by affecting plant architecture. It also plays a crucial role in high-yield wheat breeding. An association panel and a recombinant inbred line (RIL) population were used to map quantitative trait loci (QTL) for TA. Results showed that 470 significant SNPs with 10.4%–28.8% phenotypic variance explained (PVE) were detected in four replicates by a genome-wide association study (GWAS). Haplotype analysis showed that the TA_Hap_4B1 locus on chromosome 4B was a major QTL to regulate wheat TA. Ten QTL were totally detected by linkage mapping with the RIL population, and QTA.hau-4B.1 identified in six environments with the PVE of 7.88%–18.82% was a major and stable QTL. A combined analysis demonstrated that both TA_Hap_4B1 and QTA.hau-4B.1 were co-located on the same region. Moreover, QTA.hau-4B.1 was confirmed by bulked segregant RNA-Seq (BSR-Seq) analysis. Phenotypic analysis showed that QTA.hau-4B.1 was also closely related to yield traits. Furthermore, TraesCS4B02G049700 was considered as a candidate gene through analysis of gene sequence and expression. This study can be potentially used in cloning key genes modulating wheat tillering and provides valuable genetic resources for improvement of wheat plant architecture.

Association mapping unravels the genetics controlling seedling drought stress tolerance in winter wheat.

Drought is a major constraint in wheat (Triticum aestivum L.) grain yield. The present work aimed to identify quantitative trait nucleotides (QTNs)/ candidate genes influencing drought tolerance-related traits at the seedling stage in 261 accessions of a diverse winter wheat panel. Seeds from three consecutive years were exposed to polyethylene glycol 12% (PEG-6000) and a control treatment (distilled water). The Farm-CPU method was used for the association analysis with 17,093 polymorphic SNPs. PEG treatment reduced shoot length (SL) (-36.3%) and root length (RL) (-11.3%) compared with control treatments, while the coleoptile length (CL) was increased by 11% under drought conditions, suggesting that it might be considered as an indicator of stress-tolerance. Interestingly, we revealed 70 stable QTN across 17 chromosomes. Eight QTNs related to more than one trait were detected on chromosomes 1B, 2A (2), 2B, 2D, 4B, 7A, and 7B and located nearby or inside candidate genes within the linkage disequilibrium (LD) interval. For instance, the QTN on chromosome 2D is located inside the gene TraesCS2D02G133900 that controls the variation of CL_S and SL_C. The allelic variation at the candidate genes showed significant influence on the associated traits, demonstrating their role in controlling the natural variation of multi-traits of drought stress tolerance. The gene expression of these candidate genes under different stress conditions validates their biological role in stress tolerance. Our findings offer insight into understanding the genetic factors and diverse mechanisms in response to water shortage conditions that are important for wheat improvement and adaptation at early developmental stages.

Identification of a Wheat Powdery Mildew Dominant Resistance Gene in the Pm5 Locus for High-Throughput Marker-Assisted Selection.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), poses a severe threat to wheat yield and quality worldwide. Rapid identification and the accurate transference of effective resistance genes are important to the development of resistant cultivars and the sustainable control of this disease. In the present study, the wheat line AL11 exhibited high levels of resistance to powdery mildew at both the seedling and adult plant stages. Genetic analysis of the AL11 × 'Shixin 733' mapping population revealed that its resistance was controlled by a single dominant gene, tentatively designated PmAL11. Using bulked segregant RNA-Seq and molecular marker analysis, PmAL11 was mapped to the Pm5 locus on chromosome 7B where it cosegregated with the functional marker Pm5e-KASP. Sequence alignment analysis revealed that the Pm5e-homologous sequence in AL11 was identical to the reported recessive gene Pm5e in wheat landrace 'Fuzhuang 30'. It appears that PmAL11 was most probably Pm5e, but it was mediated by a dominant inheritance pattern, so it should provide a valuable resistance resource for both genetic study and wheat breeding. To efficiently use and trace PmAL11 in breeding, a new kompetitive allele-specific PCR marker AL11-K2488 that cosegregated with this gene was developed and confirmed to be applicable in the different wheat backgrounds, thus promoting its use in the marker-assisted selection of PmAL11.

Identification of TaGL1-B1 gene controlling grain length through regulation of jasmonic acid in common wheat.

Grain length is one of the most important factors in determining wheat yield. Here, a stable QTL for grain length was mapped on chromosome 1B in a F10 recombinant inbred lines (RIL) population, and the gene TaGL1-B1 encoding carotenoid isomerase was identified in a secondary large population through multiple strategies. The genome-wide association study (GWAS) in 243 wheat accessions revealed that the marker for TaGL1-B1 was the most significant among all chromosomes. EMS mutants of TaGL1 possessed significantly reduced grain length, whereas TaGL1-B1-overexpressed lines possessed significantly increased grain length. Moreover, TaGL1-B1 strongly interacted with TaPAP6. TaPAP6-overexpressed lines had significantly increased grain length. Transcriptome analysis suggested that TaPAP6 was possibly involved in the accumulation of JA (jasmonic acid). Consistently, JA content was significantly increased in the TaGL1-B1 and TaPAP6 overexpression lines. Additionally, the role of TaGL1-B1 in regulating carotenoids was verified through QTL mapping, GWAS, EMS mutants and overexpression lines. Notably, overexpression of TaGL1-B1 significantly increased wheat yield in multiple locations. Taken together, overexpression of TaGL1-B1 enhanced grain length, probably through interaction with TaPAP6 to cause the accumulation of JA that improved carotenoid content and photosynthesis, thereby resulted in increased wheat yield. This study provided valuable genes controlling grain length to improve yield and a potential insight into the molecular mechanism of modulating JA-mediated grain size in wheat.

Introgression of Seedling Plant Resistance to Leaf Rust from Agropyron cristatum into Wheat by Induced Homoeologous Recombination

Agropyron cristatum (P genome) is a Triticeae species from the wheat tertiary gene pool which has economic importance as forage and also displays traits beneficial to wheat. Resistance to leaf rust was previously mapped to the short arm of chromosome 1P (1PS) in A. cristatum by the development of a compensating Robertsonian translocation involving chromosome arm 1PS and the long arm of wheat chromosome 1B (1BL). In this study, chromosome arm 1PS was engineered using the ph1b mutation to induce 1BS/1PS homoeologous recombination and to obtain new translocations with shortened fragments of chromosome arm 1PS. Two translocations with different alien fragment sizes were identified by genomic in situ hybridization, wheat 1BS- and 1PS-specific molecular markers and gene-specific markers for glutenin, Glu-B3 and gliadin Gli-B1 seed storage protein. One translocation (called type 1) replaces a proximal segment of 1PS chromatin, and the other (called type 2) replaces a distal 1PS segment and introduces the Glu-B3 and Gli-B1 wheat storage protein loci. Six specific EST-STS markers for chromosome arm 1PS amplified PCR products in the recombinant type 2 translocation line. Resistance analysis showed that the type 2 translocation was highly resistant to a virulent race of leaf rust pathogen. The new wheat–A. cristatum translocations obtained yield material with seedling plant resistance to leaf rust and seed storage protein loci.

Genetic Basis of Resistance to Warrior (-) Yellow Rust Race at the Seedling Stage in Current Central and Northern European Winter Wheat Germplasm.

To evaluate genetic variability and seedling plant response to a dominating Warrior (-) race of yellow rust in Northern and Central European germplasm, we used a population of 229 winter wheat cultivars and breeding lines for a genome-wide association study (GWAS). A wide variation in yellow rust disease severity (based on infection types 1-9) was observed in this panel. Four breeding lines, TS049 (from Austria), TS111, TS185, and TS229 (from Germany), and one cultivar, TS158 (KWS Talent), from Germany were found to be resistant to Warrior (-) FS 53/20 and Warrior (-) G 23/19. The GWAS identified five significant SNPs associated with yellow rust on chromosomes 1B, 2A, 5B, and 7A for Warrior (-) FS 53/20, while one SNP on chromosome 5B was associated with disease for Warrior (-) G 23/19. For Warrior (-) FS 53/20, we discovered a new QTL for yellow rust resistance associated with the marker Kukri_c5357_323 on chromosome 1B. The resistant alleles G and T at the marker loci Kukri_c5357_323 on chromosome 1B and Excalibur_c17489_804 on chromosome 5B showed the largest effects (1.21 and 0.81, respectively) on the severity of Warrior (-) FS 53/20 and Warrior (-) G 23/19. Our results provide the basis for knowledge-based resistance breeding in the face of the enormous impact of the Warrior (-) race on wheat production in Europe.

Genome-wide association mapping of bread wheat genotypes using yield and grain morphology-related traits under different environments.

Depleting water resources and increasing global temperature due to climate change are major challenges to agriculture and food security worldwide. Deciphering the underlying mechanisms of traits contributing to grain development and yield is essential for the development of climate-resilient cultivars. Therefore, this study assessed 105 bread wheat genotypes grown under control, drought, and heat-stress conditions for two crop seasons and performed a genome-wide association study (GWAS) using a 90k SNP array. The genotypes showed significant trait differences under all environmental conditions. Highly significant variation was observed, with moderate (50.09%) to high (76.19%) heritability in the studied germplasms. The studied traits were all also significantly positively correlated. A total of 541 significant associations (p ≤ 10-3) between marker and trait (MTAs) were observed after crossing the FDR <0.05 threshold for all traits. Among these, 195, 179, and 167 significant MTAs were detected under control, drought, and heat-stress conditions, respectively. Under the control and drought conditions, pleiotropic loci BS00010616_51 and BS00010868_51 were observed on chromosomes 7B and 1B situated at 186.24cM and 35.47cM, respectively. Pleiotropic loci BS00010868_51, Kukri_c11154_1723, and Ex_c10068_1509 were identified on chromosomes 1B, 5B, and 2A, respectively, under control and heat stress conditions. A stable and consistent locus (Excalibur_c20796_395) on chromosome 7A, located at 372.34cM, was also linked to grain morphology and yield-related attributes in control, drought, and heat-stress conditions. The results of the current study confirmed several previously reported MTAs for the traits under consideration and identified new MTAs under harsh climatic conditions. These SNPs will aid in the discovery of novel genes in wheat. SNPs showing significant associations may be used in marker-assisted selection and allow the development of drought- and heat-tolerant genotypes with high yields to address global food security concerns.

Molecular Mapping of Biofortification Traits in Bread Wheat (Triticum aestivum L.) Using a High-Density SNP Based Linkage Map.

A set of 188 recombinant inbred lines (RILs) derived from a cross between a high-yielding Indian bread wheat cultivar HD2932 and a synthetic hexaploid wheat (SHW) Synthetic 46 derived from tetraploid Triticum turgidum (AA, BB 2n = 28) and diploid Triticum tauschii (DD, 2n = 14) was used to identify novel genomic regions associated in the expression of grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC) and thousand kernel weight (TKW). The RIL population was genotyped using SNPs from 35K Axiom® Wheat Breeder's Array and 34 SSRs and phenotyped in two environments. A total of nine QTLs including five for GPC (QGpc.iari_1B, QGpc.iari_4A, QGpc.iari_4B, QGpc.iari_5D, and QGpc.iari_6B), two for GFeC (QGfec.iari_5B and QGfec.iari_6B), and one each for GZnC (QGznc.iari_7A) and TKW (QTkw.iari_4B) were identified. A total of two stable and co-localized QTLs (QGpc.iari_4B and QTkw.iari_4B) were identified on the 4B chromosome between the flanking region of Xgwm149-AX-94559916. In silico analysis revealed that the key putative candidate genes such as P-loop containing nucleoside triphosphatehydrolase, Nodulin-like protein, NAC domain, Purine permease, Zinc-binding ribosomal protein, Cytochrome P450, Protein phosphatase 2A, Zinc finger CCCH-type, and Kinesin motor domain were located within the identified QTL regions and these putative genes are involved in the regulation of iron homeostasis, zinc transportation, Fe, Zn, and protein remobilization to the developing grain, regulation of grain size and shape, and increased nitrogen use efficiency. The identified novel QTLs, particularly stable and co-localized QTLs are useful for subsequent use in marker-assisted selection (MAS).

QTL Mapping for Root Traits and Their Effects on Nutrient Uptake and Yield Performance in Common Wheat (Triticum aestivum L.)

Wheat is one of the most important crops in the world. Mapping QTLs for root traits is essential for the selection of wheat roots desirable for the efficient acquisition of nutrients. Here, a QTL analysis for wheat root traits was performed using 142 recombinant inbred lines derived from two wheat varieties Xiaoyan 54 and Jing 411 in a soil column culture trial. The genetic map used in this study contained 470 SSR markers and covered 3438.4 cM of wheat genome. A total of 25 QTLs for root and shoot traits were detected, located at 16 marker intervals of 13 chromosomes. The percentage of phenotypic variation explained by individual QTLs varied from 6.1% to 22.0%. The QTLs regulating RDW and root distribution on chromosomes 1A, 3A, 4A, and 5B are important for root growth in both the top- and subsoils. For qRDW-1A, qRDW-3A, and qRDW-5B, the nearest markers to the QTLs were much closer than that of qRDW-4A, with the genetic distances ranging from 0.01 to 1.18 cM. Combining these three QTLs not only increased RDW and nutrient uptake, but also increased GW, SDW, and BDW under low nitrogen conditions in the field trial. Therefore, these QTLs are valuable for marker-assisted selection of wheat root traits.

Meta-QTL analysis and in-silico transcriptome assessment for controlling chlorophyll traits in common wheat.

Chlorophyll is an important plant molecule for absorbing light and transferring electrons to produce energy for photosynthesis, which has a significant impact on crop yield. To identify quantitative trait loci (QTL) controlling chlorophyll traits in wheat (Triticum aestivum L.), a comprehensive meta-analysis of 411 original QTLs for six chlorophyll traits was performed, including the evolution of soil plant analysis development (SPAD), chlorophyll content index (CCI), chlorophyll a content (Chla), chlorophyll b content (Chlb), chlorophyll content (Chl), and ratio of chlorophyll a to b (Chla/b), derived from 41 independent experiments conducted over the past two decades. Fifty-six consensus meta-QTLs (MQTLs) were detected, unevenly distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3B, 3D, 4B, 4D, 5A, 5D, 6A, 6D, 7B, and 7D. The confidence interval (CI) of the identified MQTLs was 0.18 to 15.07 cM, with an average of 5.74 cM, and 3.17-times narrower than that of the original QTLs. A total of 30 MQTLs were aligned with marker-trait associations (MTAs) reported in genome-wide association studies (GWAS) for chlorophyll traits in wheat. Based on MQTL-flanking marker information and homology analyses combined with RNA-seq data, 136 putative candidate genes were identified in MQTL regions, involved in porphyrin metabolism, photosynthesis, terpene biosynthesis, glyoxylate and dicarboxylate metabolism, and secondary metabolites. The results of this study contribute to the understanding of the genetic basis for controlling chlorophyll traits and can be used in breeding wheat with high photosynthetic efficiency.

The Genome of Fusarium oxysporum f. sp. phaseoli Provides Insight into the Evolution of Genomes and Effectors of Fusarium oxysporum Species.

Fusarium oxysporum f. sp. phaseoli, the causal agent of cowpea fusarium wilt, is a serious threat to cowpea production in China. In this study, a sample of cowpea fusarium wilt was identified as Fusarium oxysporum f. sp. phaseoli using the methods of morphological characters and molecular detection. We further reported the first genome assembly for Fusarium oxysporum f. sp. phaseoli, with 53.7 Mb genome sequence comprising 14,694 genes. Comparative genomic analysis among five Fusarium oxysporum genomes showed that four accessory chromosomes in the five Fusarium oxysporum display similar characteristics, with low sequence similarity (55.35%, vs. overall average of 81.76%), low gene density (2.18 genes/10 kb vs. 3.02 genes/Mb) and highly transposable element density (TEs) (15.01/100 kb vs. 4.89/100 kb), indicating that variable accessory chromosomes are the main source of Fusarium oxysporum evolution. We identified a total of 100 Fusarium oxysporum f. sp. phaseoli-specific effectors in the genome and found 13 specific effector genes located in large insertion or deletion regions, suggesting that insertion or deletion events can cause the emergence of species-specific effectors in Fusarium oxysporum. Our genome assembly of Fusarium oxysporum f. sp. phaseoli provides a valuable resource for the study of cowpea fusarium wilt, and the comparative genomic study of Fusarium oxysporum could contribute to the knowledge of genome and effector-associated pathogenicity evolution in Fusarium oxysporum study.

Comprehending the dynamism of B chromosomes in their journey towards becoming unselfish.

Investigated for more than a century now, B chromosomes (Bs) research has come a long way from Bs being considered parasitic or neutral to becoming unselfish and bringing benefits to their hosts. B chromosomes exist as accessory chromosomes along with the standard A chromosomes (As) across eukaryotic taxa. Represented singly or in multiple copies, B chromosomes are largely heterochromatic but also contain euchromatic and organellar segments. Although B chromosomes are derived entities, they follow their species-specific evolutionary pattern. B chromosomes fail to pair with the standard chromosomes during meiosis and vary in their number, size, composition and structure across taxa and ensure their successful transmission through non-mendelian mechanisms like mitotic, pre-meiotic, meiotic or post-meiotic drives, unique non-disjunction, self-pairing or even imparting benefits to the host when they lack drive. B chromosomes have been associated with cellular processes like sex determination, pathogenicity, resistance to pathogens, phenotypic effects, and differential gene expression. With the advancements in B-omics research, novel insights have been gleaned on their functions, some of which have been associated with the regulation of gene expression of A chromosomes through increased expression of miRNAs or differential expression of transposable elements located on them. The next-generation sequencing and emerging technologies will further likely unravel the cellular, molecular and functional behaviour of these enigmatic entities. Amidst the extensive fluidity shown by B chromosomes in their structural and functional attributes, we perceive that the existence and survival of B chromosomes in the populations most likely seem to be a trade-off between the drive efficiency and adaptive significance versus their adverse effects on reproduction.

Genome-wide association study of yield-related traits in common wheat (Triticum aestivum L.) under normal and drought treatment conditions.

The primary goal of modern wheat breeding is to develop new high-yielding and widely adaptable varieties. We analyzed four yield-related agronomic traits in 502 wheat accessions under normal conditions (NC) and drought treatment (DT) conditions over three years. The genome-wide association analysis identified 51 yield-related and nine drought-resistance-related QTL, including 13 for the thousand-grain weight (TGW), 30 for grain length (GL), three for grain width (GW), five for spike length (SL) and nine for stress tolerance index (STI) QTL in wheat. These QTL, containing 72 single nucleotide polymorphisms (SNPs), explained 2.23 - 7.35% of the phenotypic variation across multiple environments. Eight stable SNPs on chromosomes 2A, 2D, 3B, 4A, 5B, 5D, and 7D were associated with phenotypic stability under NC and DT conditions. Two of these stable SNPs had association with TGW and STI. Several novel QTL for TGW, GL and SL were identified on different chromosomes. Three linked SNPs were transformed into kompetitive allele-specific PCR (KASP) markers. These results will facilitate the discovery of promising SNPs for yield-related traits and/or drought stress tolerance and will accelerate the development of new wheat varieties with desirable alleles.

A pleiotropic QTL increased economic water use efficiency in bread wheat (Triticum aestivum L.).

Wheat is one of the most important food crops in the world and drought can severely impact on wheat productivity. The identification and deployment of genes for improved water use efficiency (WUE) can help alleviate yield loss under water limitation. In this study, a high-density genetic linkage map of wheat recombinant inbred lines (Ningchun 4 x Ningchun 27) containing 8751 specific locus amplified fragment (SLAF) tags (including 14757 SNPs), with a total map distance of 1685 cM and an average inter-marker map distance of 0.19 cM was constructed by SLAF-seq technology. The economic yield WUE and nine related traits under three water treatments was monitored over four years. The results showed that loci conditioning WUE were also associated with grain carbon isotope discrimination (CID), flag leaf chlorophyll content, plant height, 1000-grain weight, grain weight per spike and grain number per spike. One locus on chromosome 2B explained 26.3% WUE variation in multiple environments. Under good soil moisture conditions before flowering, the high CID genotype QWue.acn-2B Ningchun 27, was associated with WUE, high grain weight per spike, and kilo-grain weight. Under rain-fed conditions, the low CID genotype QWue.acn-2B Ningchun 4 tended to maintain more spike number and was associated with improved WUE and yield. The introduction of good chromosome fragments of QWue.acn-2B into elite lines by molecular marker assisted selection will boost up the cultivation of high-yield and water-saving wheat varieties.

Genome Wide Association Study of Yield and Yield-Related Traits in Elite Spring Bread Wheat Genotypes Grown under High Temperature Environment in Sudan

Genetic improvement of wheat for heat tolerance is the main breeding objective in Sudan as it is the principal limiting factor for wheat production. To this end, the availability of wheat genetic diversity is key for success. Genetic diversities and genome-wide association studies were conducted to parse the complex genetic composition of yield-related traits of 250 bread wheat genotypes which were selected from ICARDA’s advanced materials. The genotypes were evaluated under heat stress environment for two seasons (2016/17 and 2017/18) in two sowing dates (optimum and late) at the Gezira Research Farm (GRF), of the Agricultural Research Corporation (ARC), Wad Medani, Sudan. Yield levels ranged from 4016 - 5120 kg/ha for optimum and late sowing dates respectively in the first season and from 5386 - 3926 kg/ha for optimum and late sowing dates respectively in the second season. The top 20 genotypes were better than the best check in the two seasons except, Imam which ranked number 18 in the second season. Two genotypes, genotypes 27 and 37, produced high grain yield in both seasons. Wide ranges of variations among genotypes were found for yield and yield-related traits, including days to heading and maturity, plant height, number of seeds/spike, 1000 seed weight, biomass and harvest index. Genome wide association analyses were performed using 15 kSNPmarkers and the phenotypic data. A total of 282, 355 and 475 significant (P served in the first season, second season and across seasons, respectively. Markers (6B/Kukri_ c27662, 6B/.BobWhite_c23771_525, 6B/Excalibur_c32219_491, 6B/RAC875_c31299_13021302, 6B/BS00046264_51,6A/wsnp_Ex_rep_c69373_68312188, 6A/Tdurum contig12123_1650, 6BKukri_c27662_675 and 6A/BobWhite_c15802_72) on chromosomes 6B and 6A for grain yield were highly significantly associated and stable in every season and across seasons. Highly significant Marker-traits associations (MTAs) were observed for many traits including days to heading and maturity, plant height, number of seeds/spike, 1000 seed weight, biomass and harvest index. The currently identified MTAs should be further validated using other elite sets of genotypes so that they can be used for MAS in the breeding program. The high yielding and heat tolerant genotypes identified in this study will be evaluated across key locations in Sudan for potential release in Sudan. Furthermore, they will be used as parents in the breeding program for heat tolerance.

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The crops variety growing in Armenia has not been fully explored yet, hence, their genetic potential has not been revealed. Therefore, study of gliadin (Gld) locus contained in cereals’ embryo will further clarify the process of allelofunds and genotypes, homozygocity and heterozigocity, genetic similarity, genetic formula and genomic analysis of studied cultivars and wild species. The research was carried out in 2021-2022 in the educational laboratory of Food Quality Control of the Armenian National Agrarian University. The samples of the studied plants were taken from the ex-situ seed collection of the National Genebank of Agricultural Crops and their Wild Relatives of the “Scientific Center of Agro-Biotechnology” branch of the Armenian National Agrarian University. From the electrophoretic spectrum of gliadin (Gld) for the study and identification of the genetic diversity of the inventory samples of cereals diversity protein formulas were deciphered, allelotypes and genotypes, homozygosity and heterozygosity levels were determined, and genomic analysis was performed. According to the genomic analysis of the studied cereals varieties and wild relatives using protein markers, gliadin is spread into four zones: α, β, γ and ω. The genes regulating the synthesis of different parts of gliadin of α, β, γ, ω zones, are polymorphic located in chromosomes 6B(S), 1A(S), 1B(S), 1D(S), and in the case of Alti aghaj, Voskehask and Gjulgian also in 6A chromosome. There are no genes regulating the synthesis of gliadin segments in chromosome 6D(α). Research results, as genetic markers, can be used in identification and selection of studied varieties and wild species.